HEADER HYDROLASE 19-JAN-19 6NQ6 TITLE STRUCTURE & FUNCTION OF A NEW ASPARTYLGLUCOSAMINURIA VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: N(4)-(BETA-N-ACETYLGLUCOSAMINYL)-L-ASPARAGINASE; COMPND 3 CHAIN: A, C; COMPND 4 EC: 3.5.1.26; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: N(4)-(BETA-N-ACETYLGLUCOSAMINYL)-L-ASPARAGINASE; COMPND 9 CHAIN: B, D; COMPND 10 EC: 3.5.1.26; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ELIZABETHKINGIA MENINGOSEPTICA; SOURCE 3 ORGANISM_COMMON: CHRYSEOBACTERIUM MENINGOSEPTICUM; SOURCE 4 ORGANISM_TAXID: 238; SOURCE 5 GENE: NCTC10588_03193; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ELIZABETHKINGIA MENINGOSEPTICA; SOURCE 10 ORGANISM_COMMON: CHRYSEOBACTERIUM MENINGOSEPTICUM; SOURCE 11 ORGANISM_TAXID: 238; SOURCE 12 GENE: NCTC10588_03193; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.PANDE,H.C.GUO REVDAT 4 11-OCT-23 6NQ6 1 REMARK REVDAT 3 18-DEC-19 6NQ6 1 REMARK REVDAT 2 29-MAY-19 6NQ6 1 JRNL REVDAT 1 17-APR-19 6NQ6 0 JRNL AUTH S.PANDE,H.C.GUO JRNL TITL THE T99K VARIANT OF GLYCOSYLASPARAGINASE SHOWS A NEW JRNL TITL 2 STRUCTURAL MECHANISM OF THE GENETIC DISEASE JRNL TITL 3 ASPARTYLGLUCOSAMINURIA. JRNL REF PROTEIN SCI. V. 28 1013 2019 JRNL REFN ESSN 1469-896X JRNL PMID 30901125 JRNL DOI 10.1002/PRO.3607 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 80277 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4333 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5835 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 306 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4228 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.079 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.504 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4301 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4083 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5792 ; 2.214 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9468 ; 1.242 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 558 ; 6.986 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 188 ;32.794 ;24.787 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 770 ;14.365 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;14.981 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 644 ; 0.197 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4829 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 837 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2229 ; 1.378 ; 1.240 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2228 ; 1.355 ; 1.239 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2779 ; 2.010 ; 1.852 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2780 ; 2.010 ; 1.853 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2072 ; 2.294 ; 1.575 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2073 ; 2.293 ; 1.575 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3011 ; 3.380 ; 2.240 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4805 ; 4.167 ;15.650 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4794 ; 4.159 ;15.617 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6NQ6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000239215. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80277 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08000 REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2GL9 REMARK 200 REMARK 200 REMARK: RECTANGULAR CRYSTAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NACL, 0.1M HEPES (PH 7.5), 27% REMARK 280 PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.01000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 14330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -91.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 THR A 1 REMARK 465 LYS A 99 REMARK 465 PRO A 100 REMARK 465 HIS A 101 REMARK 465 THR C 1 REMARK 465 LYS C 99 REMARK 465 PRO C 100 REMARK 465 HIS C 101 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 74 NH2 ARG D 245 1.74 REMARK 500 OD1 ASP C 45 OG1 THR C 47 2.04 REMARK 500 OD1 ASP D 273 O HOH D 301 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 20 CD GLU A 20 OE1 -0.071 REMARK 500 GLY A 54 N GLY A 54 CA 0.166 REMARK 500 GLY A 54 CA GLY A 54 C 0.124 REMARK 500 VAL A 102 N VAL A 102 CA -0.144 REMARK 500 GLY B 188 N GLY B 188 CA 0.211 REMARK 500 GLY B 188 CA GLY B 188 C 0.186 REMARK 500 GLY B 188 C GLY B 188 O 0.123 REMARK 500 CYS B 270 CB CYS B 270 SG -0.140 REMARK 500 GLU C 48 CD GLU C 48 OE2 0.069 REMARK 500 GLY D 188 N GLY D 188 CA 0.249 REMARK 500 GLY D 188 CA GLY D 188 C 0.124 REMARK 500 GLY D 188 C GLY D 188 O 0.183 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU A 8 CA - CB - CG ANGL. DEV. = 14.3 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLY A 54 C - N - CA ANGL. DEV. = -15.8 DEGREES REMARK 500 ARG A 56 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 LYS A 86 CD - CE - NZ ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG A 93 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG B 180 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 GLY B 188 C - N - CA ANGL. DEV. = -23.7 DEGREES REMARK 500 GLY B 188 N - CA - C ANGL. DEV. = 18.1 DEGREES REMARK 500 ARG C 40 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG D 180 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 ILE D 187 O - C - N ANGL. DEV. = -11.2 DEGREES REMARK 500 GLY D 188 C - N - CA ANGL. DEV. = -27.0 DEGREES REMARK 500 ARG D 245 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TRP A 11 176.57 72.64 REMARK 500 ASN A 87 69.86 -116.32 REMARK 500 ALA B 189 -81.52 -115.87 REMARK 500 ILE B 197 -57.12 -130.08 REMARK 500 ASP B 281 -157.26 -139.64 REMARK 500 TRP C 11 167.39 76.72 REMARK 500 ASN C 87 73.62 -117.37 REMARK 500 ALA D 189 -75.89 -115.83 REMARK 500 ILE D 197 -55.03 -135.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 54 GLY A 55 -136.05 REMARK 500 GLY B 188 ALA B 189 -138.34 REMARK 500 GLY D 188 ALA D 189 -145.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLY B 188 11.78 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6NQ6 A 1 138 UNP A0A376EJJ1_ELIME DBREF2 6NQ6 A A0A376EJJ1 37 174 DBREF1 6NQ6 B 152 295 UNP A0A376EJJ1_ELIME DBREF2 6NQ6 B A0A376EJJ1 188 331 DBREF1 6NQ6 C 1 138 UNP A0A376EJJ1_ELIME DBREF2 6NQ6 C A0A376EJJ1 37 174 DBREF1 6NQ6 D 152 295 UNP A0A376EJJ1_ELIME DBREF2 6NQ6 D A0A376EJJ1 188 331 SEQADV 6NQ6 LYS A 99 UNP A0A376EJJ THR 135 ENGINEERED MUTATION SEQADV 6NQ6 LYS C 99 UNP A0A376EJJ THR 135 ENGINEERED MUTATION SEQRES 1 A 138 THR THR ASN LYS PRO ILE VAL LEU SER THR TRP ASN PHE SEQRES 2 A 138 GLY LEU HIS ALA ASN VAL GLU ALA TRP LYS VAL LEU SER SEQRES 3 A 138 LYS GLY GLY LYS ALA LEU ASP ALA VAL GLU LYS GLY VAL SEQRES 4 A 138 ARG LEU VAL GLU ASP ASP PRO THR GLU ARG SER VAL GLY SEQRES 5 A 138 TYR GLY GLY ARG PRO ASP ARG ASP GLY ARG VAL THR LEU SEQRES 6 A 138 ASP ALA CYS ILE MET ASP GLU ASN TYR ASN ILE GLY SER SEQRES 7 A 138 VAL ALA CYS MET GLU HIS ILE LYS ASN PRO ILE SER VAL SEQRES 8 A 138 ALA ARG ALA VAL MET GLU LYS LYS PRO HIS VAL MET LEU SEQRES 9 A 138 VAL GLY ASP GLY ALA LEU GLU PHE ALA LEU SER GLN GLY SEQRES 10 A 138 PHE LYS LYS GLU ASN LEU LEU THR ALA GLU SER GLU LYS SEQRES 11 A 138 GLU TRP LYS GLU TRP LEU LYS THR SEQRES 1 B 144 THR ILE GLY MET ILE ALA LEU ASP ALA GLN GLY ASN LEU SEQRES 2 B 144 SER GLY ALA CYS THR THR SER GLY MET ALA TYR LYS MET SEQRES 3 B 144 HIS GLY ARG VAL GLY ASP SER PRO ILE ILE GLY ALA GLY SEQRES 4 B 144 LEU PHE VAL ASP ASN GLU ILE GLY ALA ALA THR ALA THR SEQRES 5 B 144 GLY HIS GLY GLU GLU VAL ILE ARG THR VAL GLY THR HIS SEQRES 6 B 144 LEU VAL VAL GLU LEU MET ASN GLN GLY ARG THR PRO GLN SEQRES 7 B 144 GLN ALA CYS LYS GLU ALA VAL GLU ARG ILE VAL LYS ILE SEQRES 8 B 144 VAL ASN ARG ARG GLY LYS ASN LEU LYS ASP ILE GLN VAL SEQRES 9 B 144 GLY PHE ILE ALA LEU ASN LYS LYS GLY GLU TYR GLY ALA SEQRES 10 B 144 TYR CYS ILE GLN ASP GLY PHE ASN PHE ALA VAL HIS ASP SEQRES 11 B 144 GLN LYS GLY ASN ARG LEU GLU THR PRO GLY PHE ALA LEU SEQRES 12 B 144 LYS SEQRES 1 C 138 THR THR ASN LYS PRO ILE VAL LEU SER THR TRP ASN PHE SEQRES 2 C 138 GLY LEU HIS ALA ASN VAL GLU ALA TRP LYS VAL LEU SER SEQRES 3 C 138 LYS GLY GLY LYS ALA LEU ASP ALA VAL GLU LYS GLY VAL SEQRES 4 C 138 ARG LEU VAL GLU ASP ASP PRO THR GLU ARG SER VAL GLY SEQRES 5 C 138 TYR GLY GLY ARG PRO ASP ARG ASP GLY ARG VAL THR LEU SEQRES 6 C 138 ASP ALA CYS ILE MET ASP GLU ASN TYR ASN ILE GLY SER SEQRES 7 C 138 VAL ALA CYS MET GLU HIS ILE LYS ASN PRO ILE SER VAL SEQRES 8 C 138 ALA ARG ALA VAL MET GLU LYS LYS PRO HIS VAL MET LEU SEQRES 9 C 138 VAL GLY ASP GLY ALA LEU GLU PHE ALA LEU SER GLN GLY SEQRES 10 C 138 PHE LYS LYS GLU ASN LEU LEU THR ALA GLU SER GLU LYS SEQRES 11 C 138 GLU TRP LYS GLU TRP LEU LYS THR SEQRES 1 D 144 THR ILE GLY MET ILE ALA LEU ASP ALA GLN GLY ASN LEU SEQRES 2 D 144 SER GLY ALA CYS THR THR SER GLY MET ALA TYR LYS MET SEQRES 3 D 144 HIS GLY ARG VAL GLY ASP SER PRO ILE ILE GLY ALA GLY SEQRES 4 D 144 LEU PHE VAL ASP ASN GLU ILE GLY ALA ALA THR ALA THR SEQRES 5 D 144 GLY HIS GLY GLU GLU VAL ILE ARG THR VAL GLY THR HIS SEQRES 6 D 144 LEU VAL VAL GLU LEU MET ASN GLN GLY ARG THR PRO GLN SEQRES 7 D 144 GLN ALA CYS LYS GLU ALA VAL GLU ARG ILE VAL LYS ILE SEQRES 8 D 144 VAL ASN ARG ARG GLY LYS ASN LEU LYS ASP ILE GLN VAL SEQRES 9 D 144 GLY PHE ILE ALA LEU ASN LYS LYS GLY GLU TYR GLY ALA SEQRES 10 D 144 TYR CYS ILE GLN ASP GLY PHE ASN PHE ALA VAL HIS ASP SEQRES 11 D 144 GLN LYS GLY ASN ARG LEU GLU THR PRO GLY PHE ALA LEU SEQRES 12 D 144 LYS FORMUL 5 HOH *162(H2 O) HELIX 1 AA1 TRP A 11 SER A 26 1 16 HELIX 2 AA2 LYS A 30 ASP A 45 1 16 HELIX 3 AA3 VAL A 51 GLY A 55 5 5 HELIX 4 AA4 ASN A 87 LYS A 98 1 12 HELIX 5 AA5 GLY A 106 GLN A 116 1 11 HELIX 6 AA6 THR A 125 THR A 138 1 14 HELIX 7 AA7 HIS B 205 VAL B 213 1 9 HELIX 8 AA8 VAL B 213 GLN B 224 1 12 HELIX 9 AA9 THR B 227 ARG B 246 1 20 HELIX 10 AB1 ASN B 249 ILE B 253 5 5 HELIX 11 AB2 PHE C 13 SER C 26 1 14 HELIX 12 AB3 LYS C 30 ASP C 45 1 16 HELIX 13 AB4 ASN C 87 LYS C 98 1 12 HELIX 14 AB5 GLY C 106 GLN C 116 1 11 HELIX 15 AB6 THR C 125 THR C 138 1 14 HELIX 16 AB7 HIS D 205 VAL D 213 1 9 HELIX 17 AB8 VAL D 213 GLN D 224 1 12 HELIX 18 AB9 THR D 227 ARG D 246 1 20 HELIX 19 AC1 ASN D 249 ILE D 253 5 5 SHEET 1 AA1 9 GLY B 284 GLU B 288 0 SHEET 2 AA1 9 PHE B 277 ASP B 281 -1 N PHE B 277 O GLU B 288 SHEET 3 AA1 9 ILE A 6 THR A 10 -1 N SER A 9 O ALA B 278 SHEET 4 AA1 9 ILE B 153 LEU B 158 -1 O LEU B 158 N ILE A 6 SHEET 5 AA1 9 LEU B 164 THR B 170 -1 O ALA B 167 N MET B 155 SHEET 6 AA1 9 LEU A 65 MET A 70 -1 N ASP A 66 O THR B 170 SHEET 7 AA1 9 ILE A 76 MET A 82 -1 O VAL A 79 N ALA A 67 SHEET 8 AA1 9 MET A 103 VAL A 105 1 O LEU A 104 N SER A 78 SHEET 9 AA1 9 ARG D 180 VAL D 181 -1 O VAL D 181 N MET A 103 SHEET 1 AA2 5 LEU B 191 ASP B 194 0 SHEET 2 AA2 5 GLY B 198 GLY B 204 -1 O GLY B 198 N ASP B 194 SHEET 3 AA2 5 VAL B 255 ASN B 261 -1 O LEU B 260 N ALA B 199 SHEET 4 AA2 5 TYR B 266 CYS B 270 -1 O GLY B 267 N ALA B 259 SHEET 5 AA2 5 GLY B 291 PHE B 292 1 O GLY B 291 N CYS B 270 SHEET 1 AA3 8 MET C 103 VAL C 105 0 SHEET 2 AA3 8 ILE C 76 MET C 82 1 N SER C 78 O LEU C 104 SHEET 3 AA3 8 LEU C 65 MET C 70 -1 N LEU C 65 O MET C 82 SHEET 4 AA3 8 LEU D 164 THR D 170 -1 O THR D 170 N ASP C 66 SHEET 5 AA3 8 ILE D 153 LEU D 158 -1 N MET D 155 O ALA D 167 SHEET 6 AA3 8 ILE C 6 THR C 10 -1 N LEU C 8 O ILE D 156 SHEET 7 AA3 8 PHE D 277 ASP D 281 -1 O HIS D 280 N VAL C 7 SHEET 8 AA3 8 GLY D 284 GLU D 288 -1 O ARG D 286 N VAL D 279 SHEET 1 AA4 4 LEU D 191 ASP D 194 0 SHEET 2 AA4 4 GLY D 198 GLY D 204 -1 O GLY D 198 N ASP D 194 SHEET 3 AA4 4 VAL D 255 ASN D 261 -1 O GLY D 256 N THR D 203 SHEET 4 AA4 4 TYR D 266 CYS D 270 -1 O TYR D 269 N PHE D 257 CISPEP 1 LYS A 4 PRO A 5 0 -9.99 CISPEP 2 LYS C 4 PRO C 5 0 -7.53 CRYST1 46.150 96.020 61.490 90.00 90.05 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021668 0.000000 0.000019 0.00000 SCALE2 0.000000 0.010414 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016263 0.00000